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Respiratory Viruses

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Respiratory Viruses

The General Virology Laboratory (GVL) is the largest laboratory in the Laboratory of Viral Diseases. A combination of classical and molecular virology techniques are used to detect, type, subtype, and sequence for strain analysis, viruses associated with a variety of disease states. Cultured isolates from other virology laboratories throughout New York State are accepted for identification, as are primary clinical specimens for diagnosis.

A wide range of respiratory viruses are investigated in the GVL using conventional virus culture and modern molecular methods. Testing includes comprehensive surveillance programs, reference testing, respiratory outbreak investigations and cases of severe illness, particularly among return travelers from countries affected by the circulation of avian influenza or MERS coronavirus. The GVL is a WHO-collaborating laboratory for influenza virus testing and as such participates in extensive surveillance programs sampling both out-patient and hospitalized patient populations. The GVL also performs year-round influenza testing for out-of-season influenza positive confirmations and characterization and also employs a comprehensive influenza antiviral resistance testing program. The laboratory utilizes the GenMark eSensor Respiratory Virus Panel for the investigation of severe respiratory outbreaks or individual cases of severe illness. Molecular serotyping and whole genome sequencing assays are utilized for the epidemiologic tracking of viruses such as enterovirus and adenovirus; serotype data is routinely submitted to respective national databases.

Test Menu

Virus

Real-Time PCR/Real-Time RT PCR

Molecular Serotyping*

Available in the GenMark eSensor Respiratory Viral Panel (available on NPS***)

Viral Culture

Preferred Sample Type(s) for Molecular Respiratory Virus Testing

Validated Sample Types***

Notes

Adenovirus

X

X

X

X

NPS or combined NPS/OPS

URS, CSF, rectal swabs, stool, and urine

Coronavirus (NL63, OC43, HKU1, 229E)

X¥​

X**¥​

NPS or combined NPS/OPS

URS and LRS

Cytomegalovirus

X

X

Bronchial wash or NPS

Blood, bronchial wash, CSF, URS, and urine

Enterovirus (all serotypes, including coxsackievirus and echovirus)

X

X

X

NPS or combined NPS/OPS

URS, CSF, rectal swabs, and stool

Human metapneumovirus

X

X

NPS or combined NPS/OPS, BAL or sputum

URS and LRS

Human parechovirus

X¥​

X

X

NPS or combined NPS/OPS

URS, CSF, and stool

Influenza A virus (human, seasonal)

X

X

X

X

NPS or combined NPS/OPS, BAL or sputum

URS, LRS, lung tissue, and cultured viral isolates

Influenza A virus (novel)

X

X

NPS or combined NPS/OPS, BAL or sputum

URS, LRS, and lung tissue

Requires prior approval to submit

Influenza B virus

X

X

X

X

NPS or combined NPS/OPS, BAL or sputum

URS, LRS, lung tissue, and cultured viral isolates

MERS - coronavirus

X

BAL or sputum, NPS or combined NPS/OPS and serum

BAL or sputum, NPS or combined NPS/OPS, serum, and stool

Requires prior approval to submit

Parainfluenza virus (1, 2, 3)

X¥​

X

X

NPS or combined NPS/OPS

URS, and LRS

Parainfluenza virus 4

X¥​

X**¥​

X

NPS or combined NPS/OPS

URS, and LRS

SARS - coronavirus

X

BAL or sputum, NPS or combined NPS/OPS, serum and stool

BAL or sputum, NPS or Combined NPS/OPS, serum, and stool

Requires prior approval to submit

Respiratory syncytial virus

X¥​

X

X

X

NPS or combined NPS/OPS

URS, and LRS

Rhinovirus

X

X

X

X

NPS or combined NPS/OPS

URS, and cultured viral isolates

*Aside from routine influenza virus subtyping, serotyping for other viruses is available upon request for special circumstances.
**The following targets are not part of the FDA-approved GenMark Assay: NL63, OC43, HKU1, 229E and PIV-4. These targets are considered "for research use only".
***The submission of a different specimen type will require an approved Non-Permitted Laboratory form prior to testing.
¥​ This test is not currently CLEP-approved and therefore requries an approved Non-Permitted Laboratory form prior to testing.
URS-upper respiratory swab; LRS-lower respiratory swab; NPS-nasopharyngeal swab; OPS-oropharyngeal swab

Collection

Swab specimens

Must be collected and sent in liquid viral transport media

Flocked swabs are preferred. Do NOT use cotton or calcium alginate-tipped or wooden shafted swabs